Spinal cord injury (SCI) induced changes in neurological function have significant impact on the metabolism and subsequent metabolic-related disease risk in injured individuals. This metabolic-related disease risk relationship is differential depending on the anatomic level and severity of the injury, with high level anatomic injuries contributing a greater risk of glucose and lipid dysregulation resulting in type 2 diabetes and cardiovascular disease risk elevation. Although alterations in body composition, particularly excess adiposity and its anatomical distribution in the visceral depot or ectopic location in non-adipose organs, is known to significantly contribute to metabolic disease risk, changes in fat mass and fat-free mass do not fully account for this elevated disease risk in subjects with SCI. There are other negative adaptations in body composition including reductions in skeletal muscle mass and alterations in muscle fiber type, in addition to significant reduction in physical activity, that contribute to a decline in metabolic rate and increased metabolic disease risk following SCI. Recent studies in adult humans suggest cold- and diet-induced thermogenesis through brown adipose tissue metabolism may be important for energy balance and substrate metabolism, and particularly sensitive to sympathetic nervous signaling. Considering the alterations that occur in the autonomic nervous system (SNS) (sympathetic and parasympathetic) following a SCI, significant dysfunction of brown adipose function is expected. This review will highlight metabolic alterations following SCI and integrate findings from brown adipose tissue studies as potential new areas of research to pursue.